Starting phenix.real_space_refine on Wed Jul 30 16:49:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erk_19919/07_2025/9erk_19919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erk_19919/07_2025/9erk_19919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9erk_19919/07_2025/9erk_19919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erk_19919/07_2025/9erk_19919.map" model { file = "/net/cci-nas-00/data/ceres_data/9erk_19919/07_2025/9erk_19919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erk_19919/07_2025/9erk_19919.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 42 7.16 5 P 3 5.49 5 S 158 5.16 5 Na 7 4.78 5 C 8074 2.51 5 N 2063 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12667 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1433 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "B" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2394 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 315} Chain: "C" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3287 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 29, 'TRANS': 413} Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2374 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 302} Chain: "E" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1439 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "G" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1531 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 7 Unusual residues: {' NA': 3, 'FES': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Unusual residues: {'SF4': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FMN': 1, 'RBF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' NA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 199 SG CYS A 25 50.419 61.184 58.327 1.00 6.17 S ATOM 10283 SG CYS E 108 48.138 63.150 56.147 1.00 27.39 S ATOM 857 SG CYS A 113 48.117 58.742 52.699 1.00 24.80 S ATOM 9687 SG CYS E 25 50.813 57.306 55.167 1.00 19.46 S ATOM 2824 SG CYS B 200 58.968 82.975 112.703 1.00 5.95 S ATOM 2373 SG CYS B 138 59.130 76.521 113.635 1.00 2.51 S ATOM 2927 SG CYS B 213 64.447 79.670 113.512 1.00 2.10 S ATOM 2142 SG CYS B 106 60.930 79.041 107.949 1.00 4.28 S ATOM 2447 SG CYS B 148 58.258 74.896 97.137 1.00 4.62 S ATOM 2406 SG CYS B 142 60.752 74.967 103.188 1.00 2.01 S ATOM 2288 SG CYS B 125 57.802 69.816 101.081 1.00 5.42 S ATOM 2688 SG CYS B 182 54.322 75.335 101.840 1.00 5.99 S ATOM 1840 SG CYS B 58 44.107 79.507 78.029 1.00174.01 S ATOM 1797 SG CYS B 50 47.816 79.748 84.056 1.00124.56 S ATOM 1811 SG CYS B 53 43.368 77.500 83.555 1.00155.01 S ATOM 1945 SG CYS B 75 44.372 84.330 82.210 1.00171.76 S ATOM 2474 SG CYS B 152 57.145 77.380 88.892 1.00 6.80 S ATOM 2642 SG CYS B 175 51.331 80.412 88.791 1.00 57.13 S ATOM 2623 SG CYS B 172 56.034 83.996 90.312 1.00 12.14 S ATOM 2661 SG CYS B 178 54.137 79.233 94.125 1.00 8.52 S ATOM 3219 SG CYS B 252 58.927 97.775 110.214 1.00 17.08 S ATOM 3013 SG CYS B 227 53.673 101.094 110.951 1.00 24.25 S ATOM 3166 SG CYS B 246 55.465 98.894 104.879 1.00 39.75 S ATOM 3249 SG CYS B 256 62.372 91.522 115.074 1.00 24.87 S ATOM 2971 SG CYS B 220 59.393 92.062 120.562 1.00 23.30 S ATOM 2952 SG CYS B 217 57.166 87.695 116.129 1.00 26.87 S ATOM 2986 SG CYS B 223 56.623 94.217 115.458 1.00 13.79 S ATOM 3650 SG CYS B 310 61.559 113.343 107.094 1.00107.43 S ATOM 3686 SG CYS B 316 57.749 115.277 101.854 1.00103.02 S ATOM 3488 SG CYS B 289 56.502 117.495 107.341 1.00157.38 S ATOM 3668 SG CYS B 313 56.236 110.822 105.646 1.00 82.75 S ATOM 3720 SG CYS B 320 54.661 120.148 99.007 1.00168.60 S ATOM 3442 SG CYS B 282 55.259 126.658 99.454 1.00167.88 S ATOM 3423 SG CYS B 279 57.885 125.670 97.368 1.00173.26 S ATOM 3442 SG CYS B 282 55.259 126.658 99.454 1.00167.88 S ATOM 3460 SG CYS B 285 57.902 123.153 103.112 1.00166.72 S ATOM 6541 SG CYS C 369 54.841 47.472 90.675 1.00 8.45 S ATOM 6565 SG CYS C 372 54.720 41.469 93.256 1.00 3.75 S ATOM 6584 SG CYS C 375 49.949 45.176 94.554 1.00 4.00 S ATOM 6915 SG CYS C 418 55.926 46.329 96.892 1.00 4.53 S ATOM 6867 SG CYS C 411 44.585 46.331 104.997 1.00 6.69 S ATOM 6844 SG CYS C 408 43.326 51.861 101.989 1.00 0.06 S ATOM 6608 SG CYS C 379 42.689 45.920 99.024 1.00 2.91 S ATOM 6883 SG CYS C 414 48.551 48.418 100.699 1.00 6.30 S Time building chain proxies: 9.55, per 1000 atoms: 0.75 Number of scatterers: 12667 At special positions: 0 Unit cell: (91.2, 143.64, 158.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 42 26.01 S 158 16.00 P 3 15.00 Na 7 11.00 O 2320 8.00 N 2063 7.00 C 8074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 204 " pdb="FE2 FES A 204 " - pdb=" SG CYS E 25 " pdb="FE1 FES A 204 " - pdb=" SG CYS E 108 " pdb="FE1 FES A 204 " - pdb=" SG CYS A 25 " pdb="FE2 FES A 204 " - pdb=" SG CYS A 113 " pdb=" SF4 B 401 " pdb="FE4 SF4 B 401 " - pdb=" SG CYS B 106 " pdb="FE2 SF4 B 401 " - pdb=" SG CYS B 138 " pdb="FE1 SF4 B 401 " - pdb=" SG CYS B 200 " pdb="FE3 SF4 B 401 " - pdb=" SG CYS B 213 " pdb=" SF4 B 402 " pdb="FE2 SF4 B 402 " - pdb=" SG CYS B 142 " pdb="FE4 SF4 B 402 " - pdb=" SG CYS B 182 " pdb="FE3 SF4 B 402 " - pdb=" SG CYS B 125 " pdb="FE1 SF4 B 402 " - pdb=" SG CYS B 148 " pdb=" SF4 B 403 " pdb="FE2 SF4 B 403 " - pdb=" SG CYS B 50 " pdb="FE1 SF4 B 403 " - pdb=" SG CYS B 58 " pdb="FE4 SF4 B 403 " - pdb=" SG CYS B 75 " pdb="FE3 SF4 B 403 " - pdb=" SG CYS B 53 " pdb=" SF4 B 404 " pdb="FE2 SF4 B 404 " - pdb=" SG CYS B 175 " pdb="FE1 SF4 B 404 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 404 " - pdb=" SG CYS B 172 " pdb="FE4 SF4 B 404 " - pdb=" SG CYS B 178 " pdb=" SF4 B 405 " pdb="FE3 SF4 B 405 " - pdb=" SG CYS B 227 " pdb="FE4 SF4 B 405 " - pdb=" SG CYS B 246 " pdb="FE1 SF4 B 405 " - pdb=" SG CYS B 252 " pdb=" SF4 B 406 " pdb="FE2 SF4 B 406 " - pdb=" SG CYS B 220 " pdb="FE4 SF4 B 406 " - pdb=" SG CYS B 223 " pdb="FE1 SF4 B 406 " - pdb=" SG CYS B 256 " pdb="FE3 SF4 B 406 " - pdb=" SG CYS B 217 " pdb=" SF4 B 407 " pdb="FE1 SF4 B 407 " - pdb=" SG CYS B 310 " pdb="FE4 SF4 B 407 " - pdb=" SG CYS B 313 " pdb="FE2 SF4 B 407 " - pdb=" SG CYS B 316 " pdb="FE3 SF4 B 407 " - pdb=" SG CYS B 289 " pdb=" SF4 B 408 " pdb="FE4 SF4 B 408 " - pdb=" SG CYS B 285 " pdb="FE1 SF4 B 408 " - pdb=" SG CYS B 320 " pdb="FE3 SF4 B 408 " - pdb=" SG CYS B 282 " pdb="FE3 SF4 B 408 " - pdb=" SG CYS B 279 " pdb=" SF4 C 501 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 372 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 418 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 369 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 375 " pdb=" SF4 C 502 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 408 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 411 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 379 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 414 " Number of angles added : 123 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 50.8% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 62 removed outlier: 3.620A pdb=" N ALA A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.689A pdb=" N LEU A 66 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 67' Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 71 through 94 removed outlier: 3.979A pdb=" N LYS A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.579A pdb=" N ILE A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 128 through 158 Processing helix chain 'A' and resid 167 through 185 Processing helix chain 'B' and resid 2 through 28 Proline residue: B 8 - end of helix removed outlier: 3.918A pdb=" N LYS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 124 through 131 removed outlier: 3.582A pdb=" N ALA B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.762A pdb=" N LYS B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 315 through 320 removed outlier: 4.032A pdb=" N CYS B 320 " --> pdb=" O CYS B 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.718A pdb=" N SER C 20 " --> pdb=" O ARG C 17 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 21 " --> pdb=" O LYS C 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 118 through 121 removed outlier: 3.585A pdb=" N ASP C 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 122 through 134 removed outlier: 4.000A pdb=" N ALA C 126 " --> pdb=" O MET C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 removed outlier: 3.619A pdb=" N LYS C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 210 through 222 removed outlier: 3.590A pdb=" N GLY C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 240 removed outlier: 3.846A pdb=" N GLN C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY C 239 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 240 " --> pdb=" O PRO C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 240' Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 310 through 318 removed outlier: 3.616A pdb=" N VAL C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.591A pdb=" N GLY C 377 " --> pdb=" O GLY C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 393 removed outlier: 3.581A pdb=" N ILE C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 423 through 442 removed outlier: 3.701A pdb=" N ARG C 440 " --> pdb=" O ILE C 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 43 removed outlier: 3.568A pdb=" N ILE D 23 " --> pdb=" O SER D 19 " (cutoff:3.500A) Proline residue: D 33 - end of helix Processing helix chain 'D' and resid 43 through 68 removed outlier: 4.071A pdb=" N LEU D 47 " --> pdb=" O GLY D 43 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.706A pdb=" N VAL D 81 " --> pdb=" O TRP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 109 removed outlier: 4.468A pdb=" N GLY D 99 " --> pdb=" O PRO D 95 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL D 100 " --> pdb=" O TRP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 136 Processing helix chain 'D' and resid 137 through 140 removed outlier: 3.520A pdb=" N MET D 140 " --> pdb=" O PRO D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 140' Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 190 through 204 removed outlier: 3.925A pdb=" N LEU D 194 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 3.646A pdb=" N VAL D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 236 Processing helix chain 'D' and resid 238 through 245 Processing helix chain 'D' and resid 256 through 278 Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 294 through 300 removed outlier: 3.913A pdb=" N ARG D 300 " --> pdb=" O PRO D 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 4.367A pdb=" N GLY E 10 " --> pdb=" O ASN E 6 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE E 12 " --> pdb=" O THR E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 31 removed outlier: 3.694A pdb=" N THR E 27 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 57 removed outlier: 3.896A pdb=" N GLY E 37 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 90 removed outlier: 3.632A pdb=" N ALA E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'E' and resid 101 through 106 removed outlier: 4.036A pdb=" N VAL E 105 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.575A pdb=" N SER E 120 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN E 121 " --> pdb=" O ALA E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 121' Processing helix chain 'E' and resid 122 through 154 removed outlier: 3.593A pdb=" N ALA E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 151 " --> pdb=" O ILE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 192 removed outlier: 3.604A pdb=" N ALA E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE E 179 " --> pdb=" O PRO E 175 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.706A pdb=" N LYS G 6 " --> pdb=" O GLU G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 8 through 58 removed outlier: 3.660A pdb=" N LYS G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL G 14 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE G 20 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU G 34 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY G 41 " --> pdb=" O TYR G 37 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 79 Processing helix chain 'G' and resid 144 through 148 removed outlier: 3.959A pdb=" N ALA G 147 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER G 148 " --> pdb=" O ALA G 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 144 through 148' Processing helix chain 'G' and resid 149 through 156 removed outlier: 3.754A pdb=" N GLN G 154 " --> pdb=" O TRP G 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE G 155 " --> pdb=" O ASN G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 206 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 104 Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.219A pdb=" N GLU B 118 " --> pdb=" O VAL D 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 235 Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 removed outlier: 6.430A pdb=" N LYS C 4 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY C 202 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TYR C 230 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE C 204 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU C 232 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 206 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 28 removed outlier: 8.225A pdb=" N ILE C 353 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 291 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N CYS C 355 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR C 293 " --> pdb=" O CYS C 355 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N THR C 357 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 352 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER C 330 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 354 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL C 328 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C 356 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.713A pdb=" N ALA C 84 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU C 102 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL C 82 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 80 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.516A pdb=" N VAL C 74 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 155 through 156 Processing sheet with id=AB2, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.027A pdb=" N GLY G 102 " --> pdb=" O GLY G 94 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER G 96 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN G 118 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY G 122 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY G 131 " --> pdb=" O GLY G 122 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER G 124 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE G 129 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 165 through 167 removed outlier: 6.328A pdb=" N VAL G 165 " --> pdb=" O ILE G 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 586 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 4945 1.42 - 1.64: 7682 1.64 - 1.85: 171 1.85 - 2.07: 0 2.07 - 2.29: 124 Bond restraints: 12922 Sorted by residual: bond pdb=" C4 FMN D 401 " pdb=" C4A FMN D 401 " ideal model delta sigma weight residual 1.485 1.406 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C4 FMN C 503 " pdb=" C4A FMN C 503 " ideal model delta sigma weight residual 1.485 1.406 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C4 FMN G 301 " pdb=" C4A FMN G 301 " ideal model delta sigma weight residual 1.485 1.406 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" O5' FMN C 503 " pdb=" P FMN C 503 " ideal model delta sigma weight residual 1.676 1.610 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O5' FMN G 301 " pdb=" P FMN G 301 " ideal model delta sigma weight residual 1.676 1.616 0.060 2.00e-02 2.50e+03 8.88e+00 ... (remaining 12917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 17544 3.96 - 7.91: 78 7.91 - 11.87: 5 11.87 - 15.83: 0 15.83 - 19.79: 1 Bond angle restraints: 17628 Sorted by residual: angle pdb=" CB MET B 92 " pdb=" CG MET B 92 " pdb=" SD MET B 92 " ideal model delta sigma weight residual 112.70 132.49 -19.79 3.00e+00 1.11e-01 4.35e+01 angle pdb=" CA GLU G 86 " pdb=" CB GLU G 86 " pdb=" CG GLU G 86 " ideal model delta sigma weight residual 114.10 125.43 -11.33 2.00e+00 2.50e-01 3.21e+01 angle pdb=" C ILE B 65 " pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta sigma weight residual 121.97 129.77 -7.80 1.80e+00 3.09e-01 1.88e+01 angle pdb=" CA MET B 92 " pdb=" CB MET B 92 " pdb=" CG MET B 92 " ideal model delta sigma weight residual 114.10 122.44 -8.34 2.00e+00 2.50e-01 1.74e+01 angle pdb=" C THR D 153 " pdb=" N THR D 154 " pdb=" CA THR D 154 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 ... (remaining 17623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 6652 17.51 - 35.01: 798 35.01 - 52.52: 181 52.52 - 70.02: 39 70.02 - 87.53: 10 Dihedral angle restraints: 7680 sinusoidal: 2904 harmonic: 4776 Sorted by residual: dihedral pdb=" CA CYS B 289 " pdb=" C CYS B 289 " pdb=" N PRO B 290 " pdb=" CA PRO B 290 " ideal model delta harmonic sigma weight residual -180.00 -133.01 -46.99 0 5.00e+00 4.00e-02 8.83e+01 dihedral pdb=" CA ARG E 9 " pdb=" C ARG E 9 " pdb=" N GLY E 10 " pdb=" CA GLY E 10 " ideal model delta harmonic sigma weight residual 180.00 142.34 37.66 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA LEU B 45 " pdb=" C LEU B 45 " pdb=" N PRO B 46 " pdb=" CA PRO B 46 " ideal model delta harmonic sigma weight residual -180.00 -146.74 -33.26 0 5.00e+00 4.00e-02 4.42e+01 ... (remaining 7677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1822 0.065 - 0.130: 291 0.130 - 0.196: 21 0.196 - 0.261: 2 0.261 - 0.326: 1 Chirality restraints: 2137 Sorted by residual: chirality pdb=" CB VAL B 66 " pdb=" CA VAL B 66 " pdb=" CG1 VAL B 66 " pdb=" CG2 VAL B 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA GLU G 86 " pdb=" N GLU G 86 " pdb=" C GLU G 86 " pdb=" CB GLU G 86 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO B 290 " pdb=" N PRO B 290 " pdb=" C PRO B 290 " pdb=" CB PRO B 290 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2134 not shown) Planarity restraints: 2169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 45 " 0.080 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO B 46 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 289 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" C CYS B 289 " 0.044 2.00e-02 2.50e+03 pdb=" O CYS B 289 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO B 290 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 60 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C THR D 60 " -0.043 2.00e-02 2.50e+03 pdb=" O THR D 60 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU D 61 " 0.015 2.00e-02 2.50e+03 ... (remaining 2166 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3417 2.81 - 3.33: 10925 3.33 - 3.86: 19234 3.86 - 4.38: 22225 4.38 - 4.90: 39775 Nonbonded interactions: 95576 Sorted by model distance: nonbonded pdb=" OG SER D 78 " pdb=" O2' RBF D 402 " model vdw 2.289 3.040 nonbonded pdb=" O ILE B 294 " pdb=" NZ LYS B 299 " model vdw 2.291 3.120 nonbonded pdb=" O THR B 173 " pdb=" OG1 THR B 173 " model vdw 2.292 3.040 nonbonded pdb=" ND2 ASN C 268 " pdb=" O2 FMN C 503 " model vdw 2.297 3.120 nonbonded pdb=" O THR D 151 " pdb=" OG1 THR D 151 " model vdw 2.317 3.040 ... (remaining 95571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 37.330 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12967 Z= 0.209 Angle : 1.134 64.414 17751 Z= 0.394 Chirality : 0.047 0.326 2137 Planarity : 0.007 0.121 2169 Dihedral : 16.189 87.531 4630 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.04 % Favored : 92.42 % Rotamer: Outliers : 2.82 % Allowed : 17.74 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 2.47 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1676 helix: 0.83 (0.19), residues: 757 sheet: 0.71 (0.52), residues: 95 loop : -1.94 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 97 HIS 0.004 0.001 HIS D 18 PHE 0.014 0.001 PHE E 179 TYR 0.021 0.001 TYR D 263 ARG 0.001 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.16561 ( 582) hydrogen bonds : angle 6.28231 ( 1704) metal coordination : bond 0.00647 ( 43) metal coordination : angle 10.49781 ( 123) covalent geometry : bond 0.00394 (12922) covalent geometry : angle 0.72522 (17628) Misc. bond : bond 0.04704 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: B 305 ILE cc_start: -0.4554 (OUTLIER) cc_final: -0.5014 (mt) REVERT: B 327 MET cc_start: 0.6644 (mmt) cc_final: 0.6269 (mmp) REVERT: G 179 GLN cc_start: 0.7751 (tt0) cc_final: 0.7541 (tp40) outliers start: 38 outliers final: 18 residues processed: 169 average time/residue: 1.3773 time to fit residues: 252.9267 Evaluate side-chains 137 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 184 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 130 optimal weight: 0.0770 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.114502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.071281 restraints weight = 20379.939| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.63 r_work: 0.2706 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12967 Z= 0.150 Angle : 1.061 68.544 17751 Z= 0.339 Chirality : 0.044 0.222 2137 Planarity : 0.006 0.120 2169 Dihedral : 6.024 59.844 1837 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.80 % Favored : 92.72 % Rotamer: Outliers : 2.97 % Allowed : 19.01 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1676 helix: 1.60 (0.20), residues: 764 sheet: 0.67 (0.53), residues: 96 loop : -2.02 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 97 HIS 0.002 0.001 HIS D 18 PHE 0.020 0.001 PHE A 21 TYR 0.020 0.001 TYR D 263 ARG 0.001 0.000 ARG G 55 Details of bonding type rmsd hydrogen bonds : bond 0.06661 ( 582) hydrogen bonds : angle 4.47522 ( 1704) metal coordination : bond 0.00624 ( 43) metal coordination : angle 10.34655 ( 123) covalent geometry : bond 0.00336 (12922) covalent geometry : angle 0.62185 (17628) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 2.578 Fit side-chains revert: symmetry clash REVERT: B 30 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6833 (t80) REVERT: B 305 ILE cc_start: -0.0957 (OUTLIER) cc_final: -0.1777 (mt) REVERT: G 179 GLN cc_start: 0.7901 (tt0) cc_final: 0.7272 (tp40) outliers start: 40 outliers final: 17 residues processed: 156 average time/residue: 1.5921 time to fit residues: 273.0125 Evaluate side-chains 137 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 155 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 138 optimal weight: 0.0070 chunk 43 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.071276 restraints weight = 20585.678| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.64 r_work: 0.2711 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12967 Z= 0.135 Angle : 1.118 50.758 17751 Z= 0.321 Chirality : 0.044 0.172 2137 Planarity : 0.005 0.118 2169 Dihedral : 5.455 55.525 1820 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.86 % Favored : 92.84 % Rotamer: Outliers : 3.71 % Allowed : 18.49 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1676 helix: 1.94 (0.20), residues: 757 sheet: 0.67 (0.53), residues: 96 loop : -2.05 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 97 HIS 0.002 0.001 HIS D 18 PHE 0.010 0.001 PHE D 131 TYR 0.018 0.001 TYR D 263 ARG 0.006 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06059 ( 582) hydrogen bonds : angle 4.18889 ( 1704) metal coordination : bond 0.00879 ( 43) metal coordination : angle 11.41771 ( 123) covalent geometry : bond 0.00295 (12922) covalent geometry : angle 0.59083 (17628) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 118 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: B 30 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6990 (t80) REVERT: B 305 ILE cc_start: -0.1253 (OUTLIER) cc_final: -0.2059 (mt) REVERT: C 123 ASP cc_start: 0.5552 (OUTLIER) cc_final: 0.5329 (p0) REVERT: C 342 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8185 (m) REVERT: E 1 MET cc_start: 0.5056 (OUTLIER) cc_final: 0.4558 (pp-130) REVERT: G 162 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: G 179 GLN cc_start: 0.7870 (tt0) cc_final: 0.7265 (tp40) outliers start: 50 outliers final: 23 residues processed: 154 average time/residue: 1.1939 time to fit residues: 201.3816 Evaluate side-chains 139 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 73 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 160 optimal weight: 0.4980 chunk 51 optimal weight: 0.0170 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 32 optimal weight: 0.0170 chunk 107 optimal weight: 2.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.074304 restraints weight = 20498.182| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.66 r_work: 0.2767 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 12967 Z= 0.113 Angle : 1.038 45.193 17751 Z= 0.301 Chirality : 0.042 0.182 2137 Planarity : 0.005 0.116 2169 Dihedral : 5.160 51.977 1820 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.26 % Favored : 93.44 % Rotamer: Outliers : 3.19 % Allowed : 19.38 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1676 helix: 2.06 (0.20), residues: 772 sheet: 0.67 (0.53), residues: 96 loop : -1.99 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 11 HIS 0.001 0.000 HIS D 18 PHE 0.012 0.001 PHE B 30 TYR 0.020 0.001 TYR G 37 ARG 0.002 0.000 ARG G 55 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 582) hydrogen bonds : angle 3.93700 ( 1704) metal coordination : bond 0.00899 ( 43) metal coordination : angle 10.50866 ( 123) covalent geometry : bond 0.00240 (12922) covalent geometry : angle 0.56089 (17628) Misc. bond : bond 0.00051 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8385 (m-80) cc_final: 0.8170 (m-80) REVERT: B 30 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6950 (t80) REVERT: B 305 ILE cc_start: -0.1683 (OUTLIER) cc_final: -0.2454 (mt) REVERT: C 123 ASP cc_start: 0.5321 (OUTLIER) cc_final: 0.5097 (p0) REVERT: C 342 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8199 (m) REVERT: G 162 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7774 (pm20) outliers start: 43 outliers final: 19 residues processed: 154 average time/residue: 1.1452 time to fit residues: 193.9788 Evaluate side-chains 142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.068663 restraints weight = 20662.142| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.64 r_work: 0.2661 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12967 Z= 0.158 Angle : 1.058 41.917 17751 Z= 0.327 Chirality : 0.045 0.203 2137 Planarity : 0.005 0.115 2169 Dihedral : 5.133 45.634 1818 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.28 % Favored : 92.42 % Rotamer: Outliers : 3.71 % Allowed : 19.45 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1676 helix: 2.07 (0.20), residues: 769 sheet: 0.47 (0.51), residues: 106 loop : -2.06 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 11 HIS 0.003 0.001 HIS D 18 PHE 0.013 0.001 PHE B 30 TYR 0.023 0.002 TYR G 37 ARG 0.012 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.06701 ( 582) hydrogen bonds : angle 4.13070 ( 1704) metal coordination : bond 0.00739 ( 43) metal coordination : angle 10.43814 ( 123) covalent geometry : bond 0.00373 (12922) covalent geometry : angle 0.60592 (17628) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8444 (m-80) cc_final: 0.8119 (m-80) REVERT: B 30 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.7094 (t80) REVERT: B 305 ILE cc_start: -0.1003 (OUTLIER) cc_final: -0.1771 (mt) REVERT: C 123 ASP cc_start: 0.5735 (OUTLIER) cc_final: 0.5516 (p0) REVERT: C 342 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8221 (m) REVERT: E 1 MET cc_start: 0.4949 (OUTLIER) cc_final: 0.4306 (pp-130) REVERT: G 179 GLN cc_start: 0.7892 (tt0) cc_final: 0.7272 (tp40) outliers start: 50 outliers final: 28 residues processed: 148 average time/residue: 1.1769 time to fit residues: 191.2894 Evaluate side-chains 145 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 201 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 19 optimal weight: 0.0070 chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.070115 restraints weight = 20679.945| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.62 r_work: 0.2697 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12967 Z= 0.129 Angle : 1.020 39.873 17751 Z= 0.312 Chirality : 0.043 0.187 2137 Planarity : 0.005 0.115 2169 Dihedral : 5.023 44.624 1817 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.80 % Favored : 92.96 % Rotamer: Outliers : 3.19 % Allowed : 20.42 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1676 helix: 2.13 (0.20), residues: 775 sheet: 0.44 (0.50), residues: 106 loop : -2.02 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 11 HIS 0.002 0.001 HIS D 18 PHE 0.009 0.001 PHE D 131 TYR 0.026 0.001 TYR G 37 ARG 0.002 0.000 ARG B 37 Details of bonding type rmsd hydrogen bonds : bond 0.05664 ( 582) hydrogen bonds : angle 4.00521 ( 1704) metal coordination : bond 0.00652 ( 43) metal coordination : angle 10.10365 ( 123) covalent geometry : bond 0.00290 (12922) covalent geometry : angle 0.57983 (17628) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8349 (m-80) cc_final: 0.7962 (m-80) REVERT: B 30 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.7105 (t80) REVERT: B 305 ILE cc_start: -0.1534 (OUTLIER) cc_final: -0.2298 (mt) REVERT: C 123 ASP cc_start: 0.5781 (OUTLIER) cc_final: 0.5560 (p0) REVERT: C 342 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8423 (m) REVERT: E 1 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.4249 (pp-130) REVERT: G 179 GLN cc_start: 0.7916 (tt0) cc_final: 0.7295 (tp40) outliers start: 43 outliers final: 29 residues processed: 152 average time/residue: 1.1646 time to fit residues: 194.4787 Evaluate side-chains 151 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.112150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.069188 restraints weight = 20508.864| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.63 r_work: 0.2672 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12967 Z= 0.141 Angle : 1.022 37.217 17751 Z= 0.320 Chirality : 0.044 0.192 2137 Planarity : 0.005 0.114 2169 Dihedral : 5.017 39.883 1817 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.28 % Favored : 92.48 % Rotamer: Outliers : 2.75 % Allowed : 21.31 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1676 helix: 2.14 (0.20), residues: 776 sheet: 0.50 (0.51), residues: 106 loop : -2.04 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 11 HIS 0.002 0.001 HIS D 18 PHE 0.010 0.001 PHE D 131 TYR 0.027 0.002 TYR G 37 ARG 0.014 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.05990 ( 582) hydrogen bonds : angle 4.01802 ( 1704) metal coordination : bond 0.00678 ( 43) metal coordination : angle 9.93531 ( 123) covalent geometry : bond 0.00328 (12922) covalent geometry : angle 0.60229 (17628) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8314 (m-80) cc_final: 0.7898 (m-80) REVERT: B 305 ILE cc_start: -0.1502 (OUTLIER) cc_final: -0.2263 (mt) REVERT: C 123 ASP cc_start: 0.5884 (OUTLIER) cc_final: 0.5662 (p0) REVERT: C 342 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8415 (m) REVERT: E 1 MET cc_start: 0.4790 (OUTLIER) cc_final: 0.4085 (pp-130) REVERT: G 179 GLN cc_start: 0.7964 (tt0) cc_final: 0.7329 (tp40) outliers start: 37 outliers final: 26 residues processed: 145 average time/residue: 1.2156 time to fit residues: 193.7720 Evaluate side-chains 142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.067646 restraints weight = 20088.853| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.56 r_work: 0.2791 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12967 Z= 0.185 Angle : 1.051 37.466 17751 Z= 0.346 Chirality : 0.046 0.202 2137 Planarity : 0.005 0.114 2169 Dihedral : 5.228 43.197 1817 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.82 % Favored : 91.95 % Rotamer: Outliers : 2.82 % Allowed : 21.16 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1676 helix: 2.08 (0.20), residues: 767 sheet: 0.53 (0.49), residues: 112 loop : -2.12 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 11 HIS 0.003 0.001 HIS D 18 PHE 0.013 0.001 PHE D 131 TYR 0.029 0.002 TYR G 37 ARG 0.002 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.07455 ( 582) hydrogen bonds : angle 4.24599 ( 1704) metal coordination : bond 0.00838 ( 43) metal coordination : angle 9.94579 ( 123) covalent geometry : bond 0.00451 (12922) covalent geometry : angle 0.64933 (17628) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8196 (m-80) cc_final: 0.7734 (m-80) REVERT: B 212 SER cc_start: 0.7766 (m) cc_final: 0.7463 (p) REVERT: C 123 ASP cc_start: 0.6875 (OUTLIER) cc_final: 0.6641 (p0) REVERT: E 1 MET cc_start: 0.4664 (OUTLIER) cc_final: 0.3873 (pp-130) REVERT: G 179 GLN cc_start: 0.8067 (tt0) cc_final: 0.7397 (tp40) outliers start: 38 outliers final: 28 residues processed: 148 average time/residue: 1.2615 time to fit residues: 204.0442 Evaluate side-chains 144 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 143 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.113101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.070641 restraints weight = 20134.154| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.59 r_work: 0.2839 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12967 Z= 0.142 Angle : 1.017 36.317 17751 Z= 0.326 Chirality : 0.044 0.198 2137 Planarity : 0.005 0.114 2169 Dihedral : 5.067 47.959 1814 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.16 % Favored : 92.60 % Rotamer: Outliers : 2.15 % Allowed : 22.05 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1676 helix: 2.16 (0.20), residues: 771 sheet: 0.49 (0.50), residues: 106 loop : -2.09 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 11 HIS 0.002 0.001 HIS D 18 PHE 0.010 0.001 PHE D 131 TYR 0.028 0.001 TYR G 37 ARG 0.012 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.05981 ( 582) hydrogen bonds : angle 4.05221 ( 1704) metal coordination : bond 0.00679 ( 43) metal coordination : angle 9.73200 ( 123) covalent geometry : bond 0.00330 (12922) covalent geometry : angle 0.61697 (17628) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8084 (m-80) cc_final: 0.7637 (m-80) REVERT: A 164 LYS cc_start: 0.8140 (tppt) cc_final: 0.7141 (pptt) REVERT: C 123 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6533 (p0) REVERT: E 1 MET cc_start: 0.4555 (OUTLIER) cc_final: 0.3778 (pp-130) REVERT: G 179 GLN cc_start: 0.8139 (tt0) cc_final: 0.7519 (tp40) outliers start: 29 outliers final: 25 residues processed: 136 average time/residue: 1.4437 time to fit residues: 214.4900 Evaluate side-chains 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 78 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 154 optimal weight: 0.1980 chunk 124 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN C 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.114393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.072158 restraints weight = 20014.503| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.56 r_work: 0.2875 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12967 Z= 0.125 Angle : 0.995 35.974 17751 Z= 0.317 Chirality : 0.043 0.207 2137 Planarity : 0.005 0.113 2169 Dihedral : 4.937 52.569 1814 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.10 % Favored : 92.72 % Rotamer: Outliers : 2.08 % Allowed : 22.12 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1676 helix: 2.22 (0.20), residues: 777 sheet: 0.40 (0.50), residues: 108 loop : -2.01 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 11 HIS 0.002 0.001 HIS D 18 PHE 0.009 0.001 PHE D 131 TYR 0.026 0.001 TYR G 37 ARG 0.002 0.000 ARG B 328 Details of bonding type rmsd hydrogen bonds : bond 0.05247 ( 582) hydrogen bonds : angle 3.94917 ( 1704) metal coordination : bond 0.00648 ( 43) metal coordination : angle 9.49829 ( 123) covalent geometry : bond 0.00283 (12922) covalent geometry : angle 0.60576 (17628) Misc. bond : bond 0.00034 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.976 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8065 (m-80) cc_final: 0.7578 (m-80) REVERT: A 164 LYS cc_start: 0.8001 (tppt) cc_final: 0.7011 (pptt) REVERT: B 90 MET cc_start: 0.3340 (pmt) cc_final: 0.3053 (pmm) REVERT: B 212 SER cc_start: 0.7602 (m) cc_final: 0.7348 (p) REVERT: C 123 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6427 (p0) REVERT: E 1 MET cc_start: 0.4596 (OUTLIER) cc_final: 0.3797 (pp-130) REVERT: G 179 GLN cc_start: 0.7943 (tt0) cc_final: 0.7274 (tp40) outliers start: 28 outliers final: 24 residues processed: 140 average time/residue: 1.4971 time to fit residues: 231.4761 Evaluate side-chains 142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 12 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 80 optimal weight: 0.0010 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.071299 restraints weight = 20497.088| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.61 r_work: 0.2722 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12967 Z= 0.121 Angle : 0.986 35.283 17751 Z= 0.313 Chirality : 0.043 0.210 2137 Planarity : 0.005 0.112 2169 Dihedral : 4.909 55.614 1814 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.98 % Favored : 92.84 % Rotamer: Outliers : 2.08 % Allowed : 22.35 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1676 helix: 2.30 (0.20), residues: 776 sheet: 0.53 (0.50), residues: 106 loop : -1.98 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 11 HIS 0.002 0.000 HIS C 90 PHE 0.009 0.001 PHE D 131 TYR 0.026 0.001 TYR G 37 ARG 0.013 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 582) hydrogen bonds : angle 3.89286 ( 1704) metal coordination : bond 0.00618 ( 43) metal coordination : angle 9.43480 ( 123) covalent geometry : bond 0.00272 (12922) covalent geometry : angle 0.59772 (17628) Misc. bond : bond 0.00029 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11739.51 seconds wall clock time: 206 minutes 3.83 seconds (12363.83 seconds total)